Useful tools for data standards

BATMAN is an R package for estimating metabolite levels in Nuclear Magnetic Resonance spectral data using a specialised MCMC algorithm. It deconvolves peaks from 1-dimensional NMR spectra, automatically assigns them to specific metabolites from a target list and obtains concentration estimates. The Bayesian model incorporates information on characteristic peak patterns of metabolites and is able to account for shifts in the position of peaks commonly seen in NMR spectra of biological samples.

MetAssimulo is a MATLAB-based package which simulates 1H-NMR spectra of complex mixtures such as metabolic profiles. Drawing data from a metabolite standard spectral database in conjunction with concentration information input by the user or constructed automatically from the Human Metabolome Database, MetAssimulo is able to create realistic metabolic profiles containing large numbers of metabolites with a range of user-defined properties

MIDcor (Mass Isotopomer Data corrector) is an R-based computer program designed for the extraction of “pure” 13C mass isotopomer distribution of metabolites formed from artificial 13C-enriched substrates. In addition to subtraction of natural isotope distribution from raw m/z data it examines a possible overlapping m/z peaks for several metabolites, and corrects it if such an overlapping takes place.

KODAMA is an innovative method to extract new knowledge from noisy and high-dimensional data, and offers a general framework for analyzing any kind of complex data in a broad range of sciences. It is particularly suited, but not limited, to cluster metabolomic data. Ref.: http://www.pnas.org/content/111/14/5117.abstract

Identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.

This service is based on the TOPP tool FileInfo. It works with nmrML using the current development versions of the schema, mapping and CV. An HTML representation of the official MSI mapping file and the CV can be found online.

Identification of metabolites using high precision mass spectrometry. Candidate molecules of different databases are fragmented in silico and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment.

Based on both nmrML.xsd (XML Schema Definition) and CV params (such as ontologies nmrCV, UO, CHEBI ...), a converter written in Java was developed that automatically generates nmrML files, from raw files of the major NMR vendors

Xeml-Lab 1.0 is a software initially developed at the Max Planck Institute in 2008-2009, in order to provide an interactive graphical interface, allowing the design of complex experiments, and the generation of machine-readable metadata files. The main goal of the XEML project was to realize a standard for the control and documentation of experimental design and growth, with a maximum of power in terms of data processing, not only to obtain reliable molecular and physiological data, but also to make plant growth metadata amenable for studies in integrative biology. To make Xeml-Lab, easily distributable on various platforms ( Windows, Mac and Linux), and to offer a wider access to this tool to the biological community, we decided to rewrite it in C++ language. The new version Called Xeml-Lab 1.0 is now available.

linkedISA is a package to convert ISA-TAB files into RDF data relying on different semantic frameworks (OWL ontologies). For more information, please visit the linkedISA website: http://isa-tools.github.io/linkedISA/.

Provided the files are hosted on the same server your page is running on, you can just do this to load in your ISA files. Now integrated with BMC GigaScience and allows out of box rendering of ISA-Tab formatted archives for consistent and easy content exposure of experimental metadata.

pynmrML is a Python library for reading, writing and interfacing with nmrML documents. It includes nmrML bindings, nmrCV bindings, and readers and writers for several different NMR formats. It relies on the excellent NMRglue library for processing raw NMR data.

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This project is funded through European Commission COSMOS Grant EC312941